Replica-exchange methods and predictions of helix configurations of membrane proteins

Abstract

A simulation in generalized ensemble is based on a non-Boltzmann weight factor and performs a random walk in potential energy space, which allows the simulation to avoid getting trapped in states of local-minimum energy states. In this article, we review uses of the generalized-ensemble algorithms. Three well-known methods, namely, multicanonical algorithm (MUCA), simulated tempering (ST) and replica-exchange method (REM), are described first. Both Monte Carlo (MC) and molecular dynamics (MD) versions of the algorithms are given. We then present the results of the application of replica-exchange MC method to the predictions of membrane protein structures.